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    COL6A2 collagen type VI alpha 2 chain [ Homo sapiens (human) ]

    Gene ID: 1292, updated on 27-Nov-2024

    Summary

    Official Symbol
    COL6A2provided by HGNC
    Official Full Name
    collagen type VI alpha 2 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2212
    See related
    Ensembl:ENSG00000142173 MIM:120240; AllianceGenome:HGNC:2212
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UCMD1; BTHLM1; PP3610; UCMD1B; BTHLM1B
    Summary
    This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in placenta (RPKM 164.0), endometrium (RPKM 155.3) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL6A2 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46098112..46132848)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44476193..44510935)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47518026..47552762)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene proteasome subunit alpha 6 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47500021-47500530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47504842-47505342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47505343-47505843 Neighboring gene COL6A2 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12001 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:47527125-47527884 Neighboring gene uncharacterized LOC124905043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47551971-47552475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47556247-47557020 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47560109-47560298 Neighboring gene Sharpr-MPRA regulatory region 3768 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47571745-47572448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47572449-47573154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573155-47573858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573859-47574562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47574563-47575266 Neighboring gene FTCD antisense RNA 1 Neighboring gene spermatogenesis and centriole associated 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590104-47590604 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590605-47591105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47600015-47600618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47602435-47603038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47603039-47603642

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ46862, DKFZp586E1322

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to UV IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to glucose IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    collagen alpha-2(VI) chain
    Names
    collagen VI, alpha-2 polypeptide
    collagen, type VI, alpha 2
    epididymis secretory sperm binding protein
    human mRNA for collagen VI alpha-2 C-terminal globular domain

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008675.1 RefSeqGene

      Range
      5001..39731
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_476

    mRNA and Protein(s)

    1. NM_001849.4NP_001840.3  collagen alpha-2(VI) chain isoform 2C2 precursor

      See identical proteins and their annotated locations for NP_001840.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2), that differs from the other variants in the last exon, encodes the full-length protein.
      Source sequence(s)
      AP001471, AY029208, BC065509, CN352095, CN352155
      Consensus CDS
      CCDS13728.1
      UniProtKB/Swiss-Prot
      P12110, Q13909, Q13910, Q13911, Q14048, Q14049, Q16259, Q16597, Q6P0Q1, Q9UML3, Q9Y4S8
      UniProtKB/TrEMBL
      A0A384MDP3
      Related
      ENSP00000300527.4, ENST00000300527.9
      Conserved Domains (3) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
      pfam00092
      Location:8331007
      VWA; von Willebrand factor type A domain
    2. NM_058174.3NP_478054.2  collagen alpha-2(VI) chain isoform 2C2a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2a) has a different last exon than the other variants. Isoform 2C2a is 101 amino acids shorter than isoform 2C2 and 91 amino acids longer than isoform 2C2a'.
      Source sequence(s)
      AI275476, AP001471, BC065509, BM989656, CN352095, CN352155, X15977
      Consensus CDS
      CCDS13729.1
      UniProtKB/Swiss-Prot
      P12110
      Related
      ENSP00000380870.1, ENST00000397763.6
      Conserved Domains (2) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...
    3. NM_058175.3NP_478055.2  collagen alpha-2(VI) chain isoform 2C2a' precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2C2a') encodes the shortest polypeptide. The last exon in this variant results in the use of a stop codon that shortens the protein by 192 amino acids compared to the full-length protein, although the transcripts are nearly the same length.
      Source sequence(s)
      AI275476, AP001471, BC065509, BM989656, CN352095, CN352155, M34570
      Consensus CDS
      CCDS13730.1
      UniProtKB/Swiss-Prot
      P12110
      Related
      ENSP00000387115.1, ENST00000409416.6
      Conserved Domains (2) summary
      pfam01391
      Location:439498
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:612803
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      46098112..46132848
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      44476193..44510935
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)